[CP2K:823] Re: parallel distribution of data

Teodoro Laino teodor... at gmail.com
Thu Mar 13 23:39:20 UTC 2008
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Ciao Nick,

as I thought no memory leaks detected with g95 (though you may  
question about the capability of g95 in detecting memory leaks ;-))  
neither
with HMD AIX/XLF IBM. In attachment the CLEAN run produced with HMD  
library.
Will you do the bug report to the TAU guys? ;-)

teo


------------------------------------------------------------------------ 
-----------------------------------------------------
     75  OT DIIS        0.10E+00   10.32        0.0000095923     
-2136.6131157779

   *** SCF run converged in    75 steps ***


   Total electronic density (r-space):      -1079.9999999996         
0.0000000004
   Total core charge density (r-space):      1080.0000000000        
-0.0000000000
   Total charge density (r-space):                                   
0.0000000003
   Total charge density (g-space):                                   
0.0000000003

   Overlap energy of the core charge distribution:               
0.00000006083327
   Self energy of the core charge distribution:              
-5367.73348024078405
   Core Hamiltonian energy:                                   
1579.31346328265818
   Hartree energy:                                            
2198.51013049126232
   Exchange-correlation energy:                               
-546.70322937190190

   Total energy:                                             
-2136.61311577793185

  ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.):             
-2136.613479809077035
------------------------------------------------------------------------ 
-----------------------------------------------------

On 13 Mar 2008, at 23:02, Nichols A. Romero wrote:

> Let me know what you find. It could be false positive as you said.
>
> On Thu, Mar 13, 2008 at 5:56 PM, Teodoro Laino  
> <teodor... at gmail.com> wrote:
> Nick,
>
> I doubt all of these are real memory leaks.. We check it  
> carefully.. can you please post as well the input this guy used to  
> generate the report?
> I wouldn't be surprised that the whole story here will end with a  
> bug report for the TAU guys ! ;-)
>
> Teo
>
> On 13 Mar 2008, at 22:53, Nichols A. Romero wrote:
>
>> Matt,
>>
>> One of the people in our group profiled CP2K with the TAU to look  
>> for memory leaks.
>> http://www.cs.uoregon.edu/research/tau/home.php
>>
>> A number of them were found and some of them might be related to  
>> the parallel
>> distribution algorithm. I can send you the .ppk so you can read  
>> the profile file in
>> more detail. The viewer is free.
>>
>> The attached profile shows some memory leaks, specifically in  
>> distribution_methods.f90 and memory_utilities.f90, but there are  
>> others.
>>
>> MEMORY LEAK! malloc size <file=cube_utils.pp.f90, variable=info% 
>> sphere_bounds(i)%p, line=278> : PW_ENV_METHODS::PW_ENV_REBUILD  
>> [{pw_env_methods.pp.f90} {177,12}]   => CUBE_UTILS::INIT_CUBE_INFO  
>> [{cube_utils.pp.f90} {206,14}]
>>
>> MEMORY LEAK! malloc size <file=distribution_methods.pp.f90,  
>> variable=nsgf, line=885> :  
>> DISTRIBUTION_METHODS::DISTRIBUTE_MOLECULES_2D  
>> [{distribution_methods.pp.f90} {472,14}]   =>  
>> DISTRIBUTION_METHODS::DISTRIBUTE_2D_COST_MODEL  
>> [{distribution_methods.pp.f90} {809,14}]
>>
>> MEMORY LEAK! malloc size <file=distribution_optimize.pp.f90,  
>> variable=cost_cpu, line=165> :  
>> DISTRIBUTION_METHODS::DISTRIBUTE_MOLECULES_2D  
>> [{distribution_methods.pp.f90} {472,14}]   =>  
>> DISTRIBUTION_OPTIMIZE::DISTRIBUTE_2D_MONTE_CARLO  
>> [{distribution_optimize.pp.f90} {101,14}]
>>
>> MEMORY LEAK! malloc size <file=distribution_optimize.pp.f90,  
>> variable=max_cost_para, line=271> :  
>> DISTRIBUTION_METHODS::DISTRIBUTE_MOLECULES_2D  
>> [{distribution_methods.pp.f90} {472,14}]   =>  
>> DISTRIBUTION_OPTIMIZE::DISTRIBUTE_2D_MONTE_CARLO  
>> [{distribution_optimize.pp.f90} {101,14}]
>>
>> MEMORY LEAK! malloc size <file=f77_interface.pp.f90,  
>> variable=f_envs, line=249> : CP2K [{cp2k.pp.f90} {38,9}]   =>  
>> F77_INTERFACE::INIT_CP2K [{f77_interface.pp.f90} {208,14}]
>>
>> MEMORY LEAK! malloc size <file=input_section_types.pp.f90,  
>> variable=section%subsections, line=248> :  
>> INPUT_CP2K::CREATE_CP2K_ROOT_SECTION [{input_cp2k.pp.f90}  
>> {142,14}]   => INPUT_SECTION_TYPES::SECTION_CREATE  
>> [{input_section_types.pp.f90} {186,14}]
>>
>> MEMORY LEAK! malloc size <file=memory_utilities.pp.f90,  
>> variable=p, line=291> : ATOMS_INPUT::READ_ATOMS_INPUT  
>> [{atoms_input.pp.f90} {99,14}]   =>  
>> MEMORY_UTILITIES::REALLOCATE_I1 [{memory_utilities.pp.f90} {265,14}]
>>
>> MEMORY LEAK! malloc size <file=memory_utilities.pp.f90,  
>> variable=p, line=704> : BASIS_SET_TYPES::READ_GTO_BASIS_SET  
>> [{basis_set_types.pp.f90} {800,14}]   =>  
>> MEMORY_UTILITIES::REALLOCATE_R3 [{memory_utilities.pp.f90} {672,14}]
>>
>> MEMORY LEAK! malloc size <file=qs_neighbor_lists.pp.f90,  
>> variable=aux_present, line=335> : QS_ENERGY::QS_ENERGIES  
>> [{qs_energy.pp.f90} {103,14}]   =>  
>> QS_NEIGHBOR_LISTS::BUILD_QS_NEIGHBOR_LISTS  
>> [{qs_neighbor_lists.pp.f90} {172,14}]
>>
>> MEMORY LEAK! malloc size <file=realspace_grid_types.pp.f90,  
>> variable=bounds , line=1136> :  
>> REALSPACE_GRID_TYPES::RS_PW_TRANSFER  
>> [{realspace_grid_types.pp.f90} {550,14}]   =>  
>> REALSPACE_GRID_TYPES::RS_PW_TRANSFER_DISTRIBUTED  
>> [{realspace_grid_types.pp.f90} {749,14}]
>>
>> MEMORY LEAK! malloc size <file=realspace_grid_types.pp.f90,  
>> variable=bounds , line=956> : REALSPACE_GRID_TYPES::RS_PW_TRANSFER  
>> [{realspace_grid_types.pp.f90} {550,14}]   =>  
>> REALSPACE_GRID_TYPES::RS_PW_TRANSFER_DISTRIBUTED  
>> [{realspace_grid_types.pp.f90} {749,14}]
>>
>> MEMORY LEAK! malloc size <file=reference_manager.pp.f90,  
>> variable=indx, line=210> : ENVIRONMENT::CP2K_FINALIZE  
>> [{environment.pp.f90} {764,14}]   =>  
>> REFERENCE_MANAGER::PRINT_ALL_REFERENCES  
>> [{reference_manager.pp.f90} {190,14}]
>>
>> MEMORY LEAK! malloc size <file=reference_manager.pp.f90,  
>> variable=irank, line=209> : ENVIRONMENT::CP2K_FINALIZE  
>> [{environment.pp.f90} {764,14}]   =>  
>> REFERENCE_MANAGER::PRINT_ALL_REFERENCES  
>> [{reference_manager.pp.f90} {190,14}]
>>
>> MEMORY LEAK! malloc size <file=reference_manager.pp.f90,  
>> variable=ival, line=208> : ENVIRONMENT::CP2K_FINALIZE  
>> [{environment.pp.f90} {764,14}]   =>  
>> REFERENCE_MANAGER::PRINT_ALL_REFERENCES  
>> [{reference_manager.pp.f90} {190,14}]
>>
>> MEMORY LEAK! malloc size <file=topology_generate_util.pp.f90,  
>> variable=h_list, line=519> : TOPOLOGY::CONNECTIVITY_CONTROL  
>> [{topology.pp.f90} {312,14}]   =>  
>> TOPOLOGY_GENERATE_UTIL::TOPOLOGY_GENERATE_BOND  
>> [{topology_generate_util.pp.f90} {437,14}]
>>
>> On Tue, Mar 11, 2008 at 5:18 PM, Matt W <MattWa... at gmail.com>  
>> wrote:
>>
>> No, thankfully it's not related.  Looks like another overflow
>> though...thanks for pushing things!
>>
>> Matt
>>
>> On Mar 11, 9:03 pm, "Nichols A. Romero" <naro... at gmail.com> wrote:
>> > Guys,
>> >
>> > This might be related.
>> >
>> > I just tried H2O-8192.inp on 512 & 1024 cores and I received the  
>> error
>> > below.
>> >
>> > BTW, I don't have this problem with the H2O-4096.inp
>> >
>> > *
>> >  *** ERROR in distribute_molecules_2d (MODULE  
>> distribution_methods)  ***
>> >  *
>> >
>> >  *** The memory allocation for the data object <cost_ele_pair>  
>> failed. The
>> > ***
>> >  *** requested memory size is -1835008 Kbytes
>> > ***
>> >
>> >  *** Program stopped at line number 570 of MODULE  
>> distribution_methods  ***
>> >
>> >  *
>> >  *** ERROR in distribute_molecules_2d (MODULE  
>> distribution_methods)  ***
>> >  *
>> >
>> >  *** The memory allocation for the data object <cost_ele_pair>  
>> failed. The
>> > ***
>> >  *** requested memory size is -1835008 Kbytes
>> > ***
>> >
>> > On Tue, Mar 11, 2008 at 10:14 AM, Nichols A. Romero  
>> <naro... at gmail.com>
>> > wrote:
>> >
>> >
>> >
>> > > So can I. I am running that and some larger systems.
>> >
>> > > Many thanks to Matt!
>> >
>> > > On 3/11/08, Teodoro Laino <teodor... at gmail.com> wrote:
>> >
>> > > > I can confirm that with this bug-fix H2O-2048 is running  
>> nicely.
>> >
>> > > > teo
>> >
>> > > >  On 11 Mar 2008, at 12:09, Matt W wrote:
>> >
>> > > >  (not well tested though).
>> >
>> > > --
>> > > Nichols A. Romero, Ph.D.
>> > > DoD User Productivity Enhancement and Technology Transfer  
>> (PET) Group
>> > > High Performance Technologies, Inc.
>> > > Reston, VA
>> > > 443-567-8328 (C)
>> > > 410-278-2692 (O)
>> >
>> > --
>> > Nichols A. Romero, Ph.D.
>> > DoD User Productivity Enhancement and Technology Transfer (PET)  
>> Group
>> > High Performance Technologies, Inc.
>> > Reston, VA
>> > 443-567-8328 (C)
>> > 410-278-2692 (O)
>>
>>
>>
>>
>> -- 
>> Nichols A. Romero, Ph.D.
>> DoD User Productivity Enhancement and Technology Transfer (PET) Group
>> High Performance Technologies, Inc.
>> Reston, VA
>> 443-567-8328 (C)
>> 410-278-2692 (O)
>>
>>
>
>
>
>
>
>
> -- 
> Nichols A. Romero, Ph.D.
> DoD User Productivity Enhancement and Technology Transfer (PET) Group
> High Performance Technologies, Inc.
> Reston, VA
> 443-567-8328 (C)
> 410-278-2692 (O)
> >
> <CG_3x3x3.inp>

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